Problem with replacement for Vanilla jungle temple generation (carving the terrain) and new puzzle

I have problem with my enhanced Jungle Temple datapack project (it's current version of it's files can be download here: https://drive.google.com/file/d/1Ku7J3mo3NXnetKyciiI_ZPditSRyK6pL/view?usp=sharing). 
Actually I got two. One, a bit less important is with the redstone cirtcuit. I mean my new version of the puzzle(with 9 leavers) kinda breaks easily and I don't know how to fix it. I mean with keeping it compact like it is now...
Second one is way more jaring. The structure doesn't generate prooperly - part of it is supposed to generate underground (as it is leading to the added underground chambers - not yet in the files, but I have both the entry point and all 12 chambers already designed) but...despite having a structure void down there it still carves terrain around, exposing uderground part. Anyone have any ideas on how to fix it?
I got someting like this